Around 48,000 genes per sample, 12 samples on a slide
http://core-genomics.blogspot.co.uk/2014/08/seqc-kills-microarrays-not-quite.html
? or help.start()R can do simple numerical calculations
2 + 2
## [1] 4
sqrt(25)
## [1] 5
Here, sqrt is a function and the number 25 was used as an argument to the function. Functions can have multiple arguments
We can save the result of a computation as a variable using the assignment operator <-
x <- sqrt(25)
x + 5
## [1] 10
y <- x +5
y
## [1] 10
A vector can be used to combine multiple values. The resulting object is indexed and particular values can be queried using the [] operator
vec <- c(1,2,3,6)
vec[1]
## [1] 1
Calculations can be performed on vectors
vec*2
## [1] 2 4 6 12
mean(vec)
## [1] 3
sum(vec)
## [1] 12
These can be used to represent familiar tabular (row and column) data
df <- data.frame(A = c(1,2,3,6), B = c(7,8,10,12))
df
## A B
## 1 1 7
## 2 2 8
## 3 3 10
## 4 6 12
Don’t need the same data type in each column
df <- data.frame(A = c(1,2,3,6),
B = month.name[c(7,8,10,12)])
df
## A B
## 1 1 July
## 2 2 August
## 3 3 October
## 4 6 December
We can subset data frames using the [], but can specify row and column indices
df[1,2]
## [1] July
## Levels: August December July October
df[2,1]
## [1] 2
df[1,]
## A B
## 1 1 July
df[,2]
## [1] July August October December
## Levels: August December July October
Or leave the row or column index blank to get all rows and columns respectively
Each package has its own landing page. e.g. http://bioconductor.org/packages/release/bioc/html/beadarray.html. Here you’ll find;
library function. e.g. library(beadarray)Recall that data can be read into R using read.csv, read.delim, read.table etc. Several packages provided special modifications of these to read raw data from different manufacturers
limma for various two-colour platformsaffy for Affymetrix databeadarray, lumi, limma for Illumina BeadArray dataA dataset may be split into different components
In Bioconductor we will often put these data the same object for easy referencing. The Biobase package has all the code to do this.